Try changing the yellow/blue number from 4, to 6 or higher.
And go back to first numbers you posted on the first three settings.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs